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Difference between revisions of "Carbohydrate Binding Module Family 42"
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Harry Brumer (talk | contribs) (Created page with "<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> {{UnderConstruct...") |
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<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --> | ||
{{UnderConstruction}} | {{UnderConstruction}} | ||
| − | * [[Author]]: | + | * [[Author]]: ^^^Shinya Fushinobu^^^ |
* [[Responsible Curator]]: ^^^Shinya Fushinobu^^^ | * [[Responsible Curator]]: ^^^Shinya Fushinobu^^^ | ||
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== Ligand specificities == | == Ligand specificities == | ||
| − | + | CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues <cite>Miyanaga2004</cite> which are present in plant polysaccharides such as arabinoxylan, arabinan, and arabinogalactan. | |
| − | |||
| − | |||
== Structural Features == | == Structural Features == | ||
| − | + | * '''Fold:''' CBM42s have a β-trefoil fold that is similar to [[CBM13]] and R(ricin)-type lectins. The module display a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one subdomain sometimes loses its function due to mutations at critical residues for ligand binding. | |
| − | * '''Fold:''' | + | * '''Type:''' CBM42s are typical [[Carbohydrate-binding_modules|Type C CBMs]] that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans <cite>Miyanaga2006</cite>. |
| − | * '''Type:''' | + | * '''Features of ligand binding:''' The binding sites are located at side of the triangular structure of |
| − | * '''Features of ligand binding:''' Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc. | + | Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc. |
== Functionalities == | == Functionalities == | ||
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== References == | == References == | ||
<biblio> | <biblio> | ||
| − | # | + | #Miyanaga2004 pmid=15292273 |
| − | # | + | #Miyanaga2006 pmid=16846393 |
| − | |||
| − | |||
| − | |||
| − | |||
</biblio> | </biblio> | ||
[[Category:Carbohydrate Binding Module Families|CBM042]] | [[Category:Carbohydrate Binding Module Families|CBM042]] | ||
Revision as of 00:41, 13 May 2014
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Author: ^^^Shinya Fushinobu^^^
- Responsible Curator: ^^^Shinya Fushinobu^^^
| CAZy DB link | |
| http://www.cazy.org/CBM42.html |
Ligand specificities
CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues [1] which are present in plant polysaccharides such as arabinoxylan, arabinan, and arabinogalactan.
Structural Features
- Fold: CBM42s have a β-trefoil fold that is similar to CBM13 and R(ricin)-type lectins. The module display a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one subdomain sometimes loses its function due to mutations at critical residues for ligand binding.
- Type: CBM42s are typical Type C CBMs that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans [2].
- Features of ligand binding: The binding sites are located at side of the triangular structure of
Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.
Functionalities
Content in this section should include, in paragraph form, a description of:
- Functional role of CBM: Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
- Most Common Associated Modules: 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
- Novel Applications: Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.
Family Firsts
- First Identified
- Insert archetype here, possibly including very brief synopsis.
- First Structural Characterization
- Insert archetype here, possibly including very brief synopsis.
References
- Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, and Fushinobu S. (2004). Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose. J Biol Chem. 2004;279(43):44907-14. DOI:10.1074/jbc.M405390200 |
- Miyanaga A, Koseki T, Miwa Y, Mese Y, Nakamura S, Kuno A, Hirabayashi J, Matsuzawa H, Wakagi T, Shoun H, and Fushinobu S. (2006). The family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose. Biochem J. 2006;399(3):503-11. DOI:10.1042/BJ20060567 |